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You will want the camera in full manual mode so you keep a consistent exposure across all of the images. Instead of a tripod, a dolly that follows the subject perpendicularly might be better suited for this purpose.
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dpollittJan 9 '12 at 2:58

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Use a treadmill?
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drewbennJan 9 '12 at 4:52

+1 to the treadmill. Walking in place is never going to look natural for "real" walking, since it isn't.
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mattdmJan 9 '12 at 14:08

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Given the prevalence of video on cameras, can't you take a video of it? If you want it to look stop motion just drop frames from the video then.
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rfuscaJan 9 '12 at 16:43

Thanks for the suggestion of the treadmill. I tried using video but the video gets so blurry with movement, and my friend can't move slow-motion.
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VeehmotJan 9 '12 at 23:11

2 Answers
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I'm not sure you need a better camera for this. since you are downgrading the images to a pretty low quality anyway. The secret to good green screen photography is in the lighting more than in the camera. You need to light the background as evenly as possible, and use a background color that is not present in the subject's clothing. In your example blue would not work due to the shirt, but green might. You can also use a white sheet if you make sure no part of your subject gets blown specular highlights. You need to make sure your subject is not too close to the background, as it may catch reflected light from it. This is particularly important if you go with blue or green background, maybe less with white.

The camera on a tripod is a good idea, but don't expect you'll get images that will be perfectly registered. I expect you will still need to align them, but the job will be easier when the camera was fixed on a tripod.

The camera should be in manual. If you don't want to mess much with the settings just take a few test pictures in auto mode (no on-camera flash, try to use other light sources from the sides, to not create shadows on the background) and once you find one that you like switch to manual and copy the exposure settings.

I think you want to mark a spot on the floor that your subject can use to position himself for the pictures. A line does not seem too useful, since your friend isn't really walking.

My final advice (the one that might be off-topic for this site) is that you grab a good book on animation and learn the animated walk cycle. You just need to have your friend pose in those proven positions that make up natural walks in cartoons. My recommendation is the Preston Blair book, Cartoon Animation.